I have installed Blast locally and I've configured the nucleotide database to use. I want to search some sequences (from a .fastafile) in this genome. So I used blastn:
blastn -db NewDb -query input.fasta -out blast.txt
Then I added some options to require a 100% identity and no gaps:
blastn -db NewDb -query input.fasta -perc_identity 100 -ungapped -out blast.txt
But I still have some results where only a subpart of the string is matching the genome:
BLASTN 2.2.29+ […] Database: […].fasta 20 sequences; N total letters Query= Mutant M : Length=226 Score E Sequences producing significant alignments: (Bits) Value chrom19 435 3e-122 chrom2 429 1e-120 > chrom19 Length=W Score = 435 bits (226), Expect = 3e-122 Identities = 226/226 (100%), Gaps = 0/226 (0%) Strand=Plus/Plus […] > chrom2 Length=Y Score = 429 bits (223), Expect = 1e-120 Identities = 223/223 (100%), Gaps = 0/223 (0%) Strand=Plus/Plus […]
Both results have an identity score of 100%, but the second result only use 223 of the 226 bases from the input sequence.
What parameters can I use with
blastn to get only perfect matches, with 100% identity and all the nucleotide bases from the input sequence used?